Mercurial > repos > nml > staramr

comparison staramr_search.xml @ 16:4d83eccf5f81 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84
author nml
date Mon, 07 Nov 2022 17:33:35 +0000
parents be818ae858e4
children 141afacabcfa
comparison
equal deleted inserted replaced
15:be818ae858e4 16:4d83eccf5f81
1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.8.0</token> 4 <token name="@VERSION@">0.9.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">staramr</requirement> 7 <requirement type="package" version="@VERSION@">staramr</requirement>
8 <!-- The staramr conda package includes the mlst software, but the list of schemes 8 <!-- The staramr conda package includes the mlst software, but the list of schemes
9 changes depending on the version. I specify the exact version here to make sure 9 changes depending on the version. I specify the exact version here to make sure
10 the list of schemes provided is consistent --> 10 the list of schemes provided is consistent -->
11 <requirement type="package" version="2.22.0">mlst</requirement> 11 <requirement type="package" version="2.23.0">mlst</requirement>
12 </requirements> 12 </requirements>
13 <version_command>staramr --version</version_command> 13 <version_command>staramr --version</version_command>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import re 15 #import re
16 16
80 ]]></command> 80 ]]></command>
81 <inputs> 81 <inputs>
82 <param type="data" name="genomes" format="fasta" multiple="true"/> 82 <param type="data" name="genomes" format="fasta" multiple="true"/>
83 <conditional name="pointfinder_db"> 83 <conditional name="pointfinder_db">
84 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> 84 <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
85 <option value="disabled" selected="true">Disable PointFinder</option> 85 <option value="disabled" selected="true">Disable PointFinder</option>
86 <option value="campylobacter">Campylobacter</option>
87 <option value="enterococcus_faecalis">enterococcus_faecalis</option>
88 <option value="enterococcus_faecium">enterococcus_faecium</option>
89 <option value="escherichia_coli">escherichia_coli</option>
90 <option value="helicobacter_pylori">helicobacter_pylori</option>
86 <option value="salmonella">Salmonella</option> 91 <option value="salmonella">Salmonella</option>
87 <option value="campylobacter">Campylobacter</option>
88 <option value="custom">Unvalidated</option> 92 <option value="custom">Unvalidated</option>
89 </param> 93 </param>
90 <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism --> 94 <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism -->
91 <when value="disabled"/> 95 <when value="disabled"/>
96 <when value="campylobacter"/>
97 <when value="enterococcus_faecalis"/>
98 <when value="enterococcus_faecium"/>
99 <when value="escherichia_coli"/>
100 <when value="helicobacter_pylori"/>
92 <when value="salmonella"/> 101 <when value="salmonella"/>
93 <when value="campylobacter"/>
94 102
95 <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms --> 103 <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
96 <when value="custom"> 104 <when value="custom">
97 <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results."> 105 <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="Select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">
98 <option value="enterococcus_faecalis">enterococcus_faecalis</option>
99 <option value="enterococcus_faecium">enterococcus_faecium</option>
100 <option value="escherichia_coli" selected="true">escherichia_coli</option>
101 <option value="helicobacter_pylori">helicobacter_pylori</option>
102 <option value="klebsiella">klebsiella</option> 106 <option value="klebsiella">klebsiella</option>
103 <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option> 107 <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
104 <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option> 108 <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
105 <option value="plasmodium_falciparum">plasmodium_falciparum</option> 109 <option value="plasmodium_falciparum">plasmodium_falciparum</option>
106 <option value="staphylococcus_aureus">staphylococcus_aureus</option> 110 <option value="staphylococcus_aureus">staphylococcus_aureus</option>
326 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 330 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
327 </output_collection> 331 </output_collection>
328 </test> 332 </test>
329 <test> 333 <test>
330 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 334 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
331 <param name="use_pointfinder" value="custom" /> 335 <param name="use_pointfinder" value="escherichia_coli" />
332 <param name="pointfinder_custom" value="escherichia_coli" />
333 336
334 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" /> 337 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
335 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" /> 338 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
336 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> 339 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
337 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> 340 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
393 </tests> 396 </tests>
394 <help><![CDATA[ 397 <help><![CDATA[
395 staramr 398 staramr
396 ======= 399 =======
397 400
398 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes. 401 staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes.
399 402
400 Usage 403 Usage
401 ----- 404 -----
402 405
403 1. Select your genome contigs (in FASTA format). 406 1. Select your genome contigs (in FASTA format).
606 609
607 .. _staramr: https://github.com/phac-nml/staramr 610 .. _staramr: https://github.com/phac-nml/staramr
608 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db 611 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
609 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db 612 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
610 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db 613 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
611 .. _webservice: https://cge.food.dtu.dk/services/ResFinder/ 614 .. _webservices: http://www.genomicepidemiology.org/services/
612 ]]></help> 615 ]]></help>
613 <citations> 616 <citations>
614 <citation type="bibtex"> 617 <citation type="bibtex">
615 @Article{microorganisms10020292, 618 @Article{microorganisms10020292,
616 AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.}, 619 AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.},